ArticleNucleic acids research2021
Voronoia 4-ever.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations.Journal of computational chemistry · 2026Article
- Enhancing the Detection of Long-Chain Aldehydes by Peptide-Based Biosensors Through Counter-Ion Exchange.Biosensors · 2026Article
- Function and Engineering of a Food Enzyme Under Coupled High-Temperature-Pressure Conditions: Insights from Molecular Dynamics Simulation and Experimental Validation.Foods (Basel, Switzerland) · 2025Article
- Hidden route of protein damage through oxygen-confined photooxidation.Nature communications · 2024Article
- Long-chain fatty acids block allergic reaction against lipid transfer protein Sola l 7 from tomato seeds.Protein science : a publication of the Protein Society · 2024Article
- MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts.Nucleic acids research · 2024Article
- Structural Landscape of nsp Coding Genomic Regions of SARS-CoV-2-ssRNA Genome: A Structural Genomics Approach Toward Identification of Druggable Genome, Ligand-Binding Pockets, and Structure-Based Druggability.Molecular biotechnology · 2024Article
- Influence of protein nativity on the stability of bovine serum albumin coated microbubbles.iScience · 2024Article
- Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection.Science (New York, N.Y.) · 2024Article
- MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS.bioRxiv : the preprint server for biology · 2024Article
- Inside Out Computational Redesign of Cavities for Improving Thermostability and Catalytic Activity ofApplied and environmental microbiology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present an updated version of the Voronoia service that enables fully automated analysis of the atomic packing density of macromolecules. Voronoia combines previous efforts to analyse 3D protein and RNA structures into a single service, combined with state-of-the-art online visualization. Voronoia uses the Voronoi cell method to calculate the free space between neighbouring atoms to estimate van der Waals interactions. Compared to other methods that derive van der Waals interactions by calculating solvent-free surfaces, it explicitly considers volume or packing defects. Large internal voids refer either to water molecules or ions unresolved by X-ray crystallography or cryo-EM, cryptic ligand binding pockets, or parts of a structural model that require further refinement. Voronoia is, therefore mainly used for functional analyses of 3D structures and quality assessments of structural models. Voronoia 4-ever updates the database of precomputed packing densities of PDB entries, allows uploading multiple structures, adds new filter options and facilitates direct access to the results through intuitive display with the NGL viewer. Voronoia is available at: htttp://proteinformatics.org/voronoia.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.